Skip to contents

Changelog

Source: NEWS.md

Rogue v2.2.0 (2026-03-20)

CRAN release: 2026-03-25

Performance

  • TipInstability() operates on the lower triangle of distance matrices only, halving the work for row statistics (rowMads, rowVars, rowMedians).

  • New batch C function LOG_GRAPH_GEODESIC_MULTI computes log-geodesic distances for all trees in a single .Call(), reusing one interim buffer and returning lower-triangle entries directly.

  • Cache-friendly extraction loop in graph_geodesic.c (stride-1 access instead of stride-all_nodes).

  • Auto-enable OpenMP parallelism in Rfast operations (rowMads, rowVars) when the distance matrix exceeds 1 000 rows.

  • Use Rfast::rowMedians() in place of matrixStats::rowMedians().

  • RogueTaxa() now calls .PrepareTrees() once and passes .prepared = TRUE to QuickRogue() / Roguehalla(), avoiding redundant tree preparation.

  • QuickRogue() precomputes information upper bounds for all iterations rather than recomputing each step.

Rogue v2.1.7 (2025-07-01)

CRAN release: 2025-07-01

  • Improve tip instability calculation in identical tree sets (#29).

  • Improve variable protection.

Rogue v2.1.6 (2023-11-29)

CRAN release: 2023-11-29

  • Legend annotations in documentation.
  • Disable parallel evaluation by default in TipInstability(), adding parallel parameter to allow user to override.
  • Use format string in REprintf().

Rogue v2.1.5 (2023-03-20)

CRAN release: 2023-03-20

  • Call C functions using symbols, not strings.

Rogue v2.1.4 (2023-01-16)

CRAN release: 2023-01-16

  • C2X compliant function prototypes.

  • Remove unused sprintf() calls.

Rogue v2.1.3 (2022-09-26)

CRAN release: 2022-09-26

  • ColByStability() gains pal argument to allow specification of custom palettes.

Rogue v2.1.2 (2022-08-16)

CRAN release: 2022-08-16

  • Faster rogue detection when edge lengths provided, per report by Joe Keating.

  • Don’t list neverDrop in QuickRogue(fullSeq = TRUE).

Rogue v2.1.1 (2022-07-20)

CRAN release: 2022-07-20

  • Handle ColByStability(trees = NULL).

Rogue v2.1.0 (2022-01-13)

CRAN release: 2022-01-13

  • Early termination of QuickRogue() when no further improvement possible.

  • Cophenetic() renamed to the more accurate GraphGeodesic().

  • Calculate information content of consensus trees with p > 0.5 (#15).

  • Improve support for multiPhylo objects.

  • New vignette detailing rogue detection with Bayesian tree samples.

Rogue v2.0.0 (2021-09-13)

CRAN release: 2021-09-13

  • Information theoretic rogue detection (per Smith, 2022).

Rogue v1.0.0 (2021-06-28)

CRAN release: 2021-07-01

  • R interface to RogueNaRok.